Reverse Dependencies of scikit-bio

The following projects have a declared dependency on scikit-bio:

• allfreqs — Calculate allele frequency from a sequence multialignment.
• birdman — Framework for differential microbiome abundance using Bayesian inference
• calour — CALOUR: exploratory and interactive microbiome analyses based on heatmap
• codon-degeneracy — Routines for the extraction of degenerate sides and estimation of numbers neutral substitutions from sequences and alignments.
• covigator — no summary
• DEICODE — Robust Aitchison compositional biplots from sparse count data
• Dellingr — Error supression and variant calling pipeline for Illumina sequencing data
• dms2dfe — Pipeline to analyse Deep Mutational Scanning (DMS) experiments in terms of Distribution of Fitness Effects (DFE)
• dpi-sc — An end-to-end single-cell multimodal analysis model with deep parameter inference.
• DRAM-bio — Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
• flight-genome — flight - metagenomic binner and variant clusterer.
• gemelli — Robust Aitchison Tensor Decomposition for sparse count data
• genomics-data-index — Indexes genomics data (nucleotide variants, kmers, MLST) for fast querying of features.
• gfpa — Gene function and cell surface protein association analysis based on single-cell multiomics data.
• gneiss — Compositional data analysis tools and visualizations
• hitac — Hierarchical taxonomic classifier.
• ingenannot — InGenAnnot: Inspection of Gene Annotation
• mashpit — A sketch-based surveillance platform
• memo-ms — Python package to perform MS2 Based Sample Vectorization and visualization
• metadex — no summary
• metagenomix — metagenomix is a pipeline of pipelines to conduct metagenomic analyses on Slurm/Torque
• MicroView — Generate reports from metagenomics data
• microwinebar — MicroWineBar
• moonstone — Utilities for metagenomics data analysis using machine learning.
• ms-tools — Functions that I commonly use
• openclean-pattern — Library for pattern and anomalous pattern detection
• phylotypes — Group phylogenetically placed sequence variants into phylotypes
• piemmer — A algorithm that simplify the input for principal component analysis
• pygenprop — A python library for programmatic usage of EBI InterPro Genome Properties.
• pymantra — Reaction-Centred Metabolic Network Analysis
• pymgpipe — Community level microbiome metabolic modeling in Python
• q2-umap — Sample Embedding with UMAP
• qurro — Visualizes differentially ranked features and log-ratios of their sample abundances
• rarefaction — Rarefaction and Accumulation for Metagenomic datasets
• redbiom — no summary
• rhapsody — Microbe-metabolite interactions through neural networks
• RoboMax — python code for versatile Functional Ontology Assignments for Metagenomes via Hidden Markov Model (HMM) searching with environmental focus of shotgun meta'omics data
• scafold — A Python implementatino of the SCA method
• scikit-bio-parasail — no summary
• scirpy — Python library for single-cell adaptive immune receptor repertoire (AIRR) analysis
• SCNIC — A tool for finding and summarizing modules of highly correlated observations in compositional data
• sourcepredict — Classification and prediction of the origin of metagenomic samples
• strainge — Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains.
• taxontabletools — TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data
• TCRcloud — TCRcloud is an AIRR visualization and comparison tool
• tmap — A topological data analysis framework implementing the TDA Mapper algorithm for population-scale microbiome data analysis
• treeCl — Phylogenetic Clustering Package
• TreeOrdination — Projection of High-Dimensional Data Using Multivariate Decision Trees and UMAP